Publications
You can also find my work on my Google Scholar profile.
Articles and Manuscripts
- Ekim, B., Berger, B., Chikhi, R., Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer. Cell Systems, 12: 1-11 (2021).
- Ekim, B., Berger, B., Orenstein, Y., A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets. Proceedings of the 24th International Conference in Computational Molecular Biology (RECOMB 2020), 37-53 (2020).
- Kuzu, A.T., Berenji, K.R., Ekim, B.C., Bakkal, M., The thermal modeling of deep-hole drilling process under MQL condition. Journal of Manufacturing Processes, 29: 194-203 (2017).
- Ekim, B., A novel entropy-based hierarchical clustering framework for ultrafast protein structure search and alignment, arXiv preprint, 1701.01975 (2017).
- Bakkal, M., Bodur, M.S., Sonmez, H.E., Ekim, B.C., The effect of chemical treatment methods on the outdoor performance of waste textile fiber-reinforced polymer composites. Journal of Composite Materials, 51: 2009-2021 (2016).
Conferences, Workshops, and Seminars
- Approximate pattern counting in de Bruijn graphs is #W[1]-hard. Data Structures in Bioinformatics (DSB) 2022, Dusseldorf, Germany, June 2022.
- Minimizer-space de Bruijn graphs. 25th International Conference in Computational Molecular Biology (RECOMB 2021), Padova, Italy, May 2021.
- A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets. 24th International Conference in Computational Molecular Biology (RECOMB 2020), Padova, Italy, May 2020.
- Computing universal hitting sets for sequence analysis: Methods and applications. Sabanci University Program for Undergraduate Research (PURE) Seminar Series, Istanbul, Turkey, July 2019.
- Applications of universal hitting sets (UHS) in sequence analysis. Webinar for International Society for Computational Biology (ISCB) Regional Student Group (RSG) Turkey, November 2019.
- A novel entropy-based hierarchical clustering framework for ultrafast protein structure search and alignment. 2nd International Symposium on Multidisciplinary Studies and Innovative Technologies (ISMSIT), Ankara, Turkey, October 2018.
- Haplotype-aware de novo genome assembly: Novel approaches and applications. Istanbul University Bioinformatics Seminar Series, Istanbul, Turkey, October 2018.
Contributed Posters
- Fast detection of maximal exact matches with universal k-mer sampling. International Symposium on Health Informatics and Bioinformatics (HIBIT), Izmir, Turkey, October 2019.
- Memory-efficient parallel algorithms for approximating compact universal hitting sets. Workshop on Algorithms in Bioinformatics (WABI), Niagara Falls, NY, September 2019.
- Parallelizing algorithms for universal hitting sets. 7th Annual Broad-ISF Symposium, Jerusalem, Israel, July 2019.
- Parallel algorithms for approximating compact universal hitting sets. MIT Biology Undergraduate Student Association (BUSA) Life Sciences Undergraduate Poster Symposium, May 2019.
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